ASMS_2024_DIA/utils.py at main · RobbinBouwmeester/ASMS_2024_DIA · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
import pyopenms as pms
import random


def tryptic_digest_pyopenms(
    file_path,
    min_len=5,
    max_len=50,
    missed_cleavages=2,
    decoy_method="reverse",
    decoy_prefix="rev_",
    seq_types=["original", "decoy"],
):
    # Read the FASTA file
    fasta = pms.FASTAFile()
    entries = []
    fasta.load(file_path, entries)

    # Set up the enzyme digestion
    digestor = pms.ProteaseDigestion()
    digestor.setEnzyme("Trypsin")
    digestor.setMissedCleavages(missed_cleavages)

    peptides = []
    for entry in entries:
        # Process both original and decoy sequences
        for seq_type in seq_types:
            if seq_type == "original":
                protein_sequence = str(entry.sequence)
            else:
                if decoy_method == "reverse":
                    protein_sequence = str(entry.sequence)[::-1]
                elif decoy_method == "scramble":
                    seq_list = list(str(entry.sequence))
                    random.shuffle(seq_list)
                    protein_sequence = "".join(seq_list)
                else:
                    raise ValueError(
                        "Invalid decoy method. Choose 'reverse' or 'scramble'."
                    )

            protein_name = entry.identifier.split()[
                0
            ]  # Adjust based on your FASTA format

            # Perform the tryptic digest
            result = []
            digestor.digest(pms.AASequence.fromString(protein_sequence), result)

            for peptide in result:
                peptide_sequence = str(peptide.toString())
                len_pep_seq = len(peptide_sequence)
                start = protein_sequence.find(peptide_sequence)
                end = start + len_pep_seq
                if "X" in peptide_sequence:
                    continue
                if len_pep_seq >= min_len and len_pep_seq <= max_len:
                    if seq_type == "original":
                        peptides.append(
                            (
                                protein_name,
                                start,
                                end,
                                f"{protein_name}|{start}|{end}",
                                peptide_sequence,
                            )
                        )
                    else:
                        peptides.append(
                            (
                                f"{decoy_prefix}{protein_name}",
                                start,
                                end,
                                f"{decoy_prefix}{protein_name}|{start}|{end}",
                                peptide_sequence,
                            )
                        )

    return peptides